Pathogenicity,sequence and phylogenetic analysis of <Emphasis Type="Italic">Malaysian Chicken anaemia virus</Emphasis> obtained after low and high passages in MSB-1 cells

Summary. Specific-pathogen-free (SPF) chickens inoculated with low passage Chicken anaemia virus (CAV), SMSC-1 and 3-1 isolates produced lesions suggestive of CAV infection. Repeated passages of the isolates in cell culture until passage 60 (P60) and passage 123 produced viruses that showed a significantly reduced level of pathogenicity in SPF chickens compared to the low passage isolates. Sequence comparison indicated that nucleotide changes in only the coding region of the P60 passage isolates were thought to contribute to virus attenuation. Phylogenetic analysis indicated that SMSC-1 and 3-1 were highly divergent, but their P60 passage derivatives shared significant homology to a Japanese isolate A2.     

Isolation of bluetongue virus serotype 1 (BTV-1) from goats and its phylogenetic relationship to other BTV-1 isolates worldwide based on full-length sequence of genome segment-2

Eight bluetongue viruses (BTV) were isolated in BHK-21 cell culture from blood of goats suffering from peste des petits ruminants. These viruses were identified as BTV serotype 1 (BTV-1) by RT-PCR using VP2-gene-based primers coupled with sequencing of the PCR products. All of the isolates showed similar genome migration profile in 8% polyacrylamide gel electrophoresis. The genome segment-2 (seg-2) of one isolate (MKD18/India/2008) was amplified piecemeal by overlapping PCR, and the products were sequenced to obtain full-length seg-2. Phylogenetic analysis based on the seg-2 sequence revealed that MKD18 is closely related to Australian BTV-1 isolates, with 86.3–86.8% nucleotide identity. Phylogenetic analysis based on the partial sequence of seg-2 (541 bp, nucleotides 1,304–1,844) showed that the Indian BTV-1 isolates, namely, MKD18, Avikanagar, Sirsa-3 and Chennai, are very closely related to each other, with more than 99.6% nucleotide identity. Although a high degree of similarity exists, the Indian BTV-1 isolates collected over the past 25 years should be studied to demonstrate the co-existence of different VP2 antigenic profiles.     

Characterisation of New Zealand isolates of infectious bursal disease virus

Isolates of infectious bursal disease virus (IBDV) were obtained from domestic poultry in New Zealand in 1997 and 1998. An in-vivo pathogenicity study carried out in specific pathogen free (SPF) chickens demonstrated the low virulence of one of the virus isolates. The nucleotide sequences of the hypervariable region of the VP2 gene of two isolates were determined and compared with published sequences of strains from other countries. The deduced amino acid sequence of the two New Zealand IBDV isolates showed 100% identity with each other, suggesting that little genetic drift had occurred. Phylogenetic analysis showed that the New Zealand isolates were more closely related to two attenuated IBDV strains (Cu1 and PBG98) than to classical (STC and 52/70), very virulent (DV86), variant (variant E) or Australian (002-73) strains. The results support the hypothesis that an attenuated strain of the virus was inadvertently introduced into the NZ poultry population in 1993.     

Sequence analysis of the VP2 gene hypervariable region of infectious bursal disease viruses from India

Attempts have been made to characterize infectious bursal disease virus (IBDV) isolates collected from different parts of India during 1993 to 1999. Phylogenetic analysis was performed on a sequence generated by cycle sequencing comprising the variable region of the VP2 gene of 14 isolates. Indian IBDV isolates had divergence of 0.2 to 4.3% at nucleotide and 0 to 2.2% at amino acid levels among themselves. Nine nucleotide changes were found in Indian IBDV field isolates, resulting in the four specific amino acid changes at 222P-A, 256V-I, 294L-I and 299N-S, reported regularly in very virulent isolates. One of the Indian IBDV isolates, UP1/99, had change D to N at position 212 in the first hydrophilic region. The serine-rich heptapeptide sequence 'SWSASGS' was conserved in all the isolates. Phylogenetically, all Indian field isolates were found to be closely related to very virulent IBDV isolates from Europe, Japan, China and Israel.     

Relationships amongst bluetongue viruses revealed by comparisons of capsid and outer coat protein nucleotide sequences

Sequence data from the gene segments coding for the capsid protein. VP3, of all eight Australian bluetongue virus serotypes were compared. The high degree of nucleotide sequence homology for VP3 genes amongst BTV isolates from the same geographic region supported previous studies (Gould, 1987; 1988b, c; Gould et al., 1988b) and was proposed as a basis for "topotyping" a bluetongue virus isolate (Gould et al., 1989). The complete nucleotide sequences which coded for the VP2 outer coat proteins of South African BTV serotypes 1 and 3 (vaccine strains) were determined and compared to cognate gene sequences from North American and Australian BTVs. These VP2 comparisons demonstrated that BTVs of the same serotype, but from different geographical regions, were closely related at the nucleotide and amino acid levels. However, close inter-relationships were also demonstrated amongst other BTVs irrespective of serotype or geographic origin. These data enabled phylogenic relationships of the BTV serotypes to be analysed using VP2 nucleotide sequences as a determinant.     

Characterisation of a chicken anaemia virus variant population that resists neutralisation with a group-specific monoclonal antibody

Summary.  A variant population of chicken anaemia virus (CAV), termed P310 2A9-resist, that resists neutralisation by the monoclonal antibody (MAb) 2A9, was selected from Cux-1 virus that had been passaged 310 times (P310) in MDCC-MSB1 cells. Substantially higher concentrations of MAb 2A9 were required to neutralise the selected virus compared to those required to neutralise a low-passage (P13) Cux-1 isolate. Virus neutralisation tests showed that serum from chickens infected with the P310 2A9-resist virus neutralised P13 virus and that serum from chickens infected with P13 virus conversely neutralised the P310 2A9-resist virus. MDCC-MSB1 cells infected with the P310 2A9-resist virus produced no staining with low dilutions (1:100) of Mab 2A9 in an indirect immunofluorescence (IF) test, whereas cells infected with P13 virus reacted positively at high MAb dilutions (1:80,000). Experimental infections of 1-day-old SPF chicks showed that the P310 2A9-resist virus was substantially attenuated. Chimaeric viruses constructed using PCR-amplified regions from the P310 2A9-resist and a pathogenic low-passage cloned Cux-1 isolate showed that the reduced MAb reactivity and attenuation exhibited by the P310 2A9-resist virus were mainly associated with a region encoding the N-terminal half of the 50 kDa capsid protein VP1 and C-terminal regions of VP2 and VP3. The nucleotide sequence of the protein-coding region of the P310 2A9-resist virus is reported and the amino acid sequences of the 3 encoded proteins compared with those of other Cux-1 isolates. Received June 19, 2000 Accepted October 24, 2000     

Investigation of the unstable attenuation exhibited by a chicken anaemia virus isolate.

An attenuated chicken anaemia virus (CAV) isolate, cloned isolate 10, which was molecularly cloned from the Cuxhaven-1 CAV after 173 cell-culture passages, was shown previously to recover pathogenicity following 10 passages in young chicks. The consensus nucleotide sequence of the 'revertant' (Rev) virus, present as a tissue homogenate, differed from cloned isolate 10 at a single nucleotide residue (nucleotide 1739) that changed amino acid 287 of the capsid protein from alanine to aspartic acid. Subjecting Rev virus to 10 cell-culture passages reselected viruses with an alanine at this amino acid position. Experimental infections using a molecularly cloned Rev virus isolate demonstrated that the mutation at nucleotide 1739 was not in itself responsible for the recovery of pathogenicity exhibited by the Rev virus. Additional sequence analyses of cloned amplicons provided evidence that the Rev virus population comprised minor, genetically different subpopulations, and provided an indication of CAV's potential for genetic change.     

Characterization of variable genomic regions of Indian white spot syndrome virus

A recent study examining genetic variations among the 3 completely sequenced white spot syndrome virus (WSSV) genomes isolated from China, Thailand and Taiwan revealed five major differences among them. Of these differences, a deletion region between ORF 23/24 and a variable region of ORF14/15 prone to recombination were of particular evolutionary significance. Focusing on these regions, 81 WSSV isolates from India were characterized by sequencing polymerase chain reaction (PCR) amplicons. The Indian strains carried a 10,970 bp deletion in the ORF 23/24 region relative to WSSV-TW and WSSV-TH-96-II. Analysis of the ORF 14/15 regions revealed two novel strains of WSSV with unique sequences which could have evolved by recombination. None of the WSSV isolates had a transposase sequence or VP35 gene as reported for Taiwan isolates. The Indian strains were closely related to Thailand strains suggesting movement of a putative ancestor from Thailand to other parts of the world including India.     

Molecular cloning of an attenuated chicken anaemia virus isolate following repeated cell culture passage.

The pathogenicity of the Cux-1 isolate of chicken anaemia virus (CAV) was substantially reduced following large numbers (50 to 173) of passages in MDCC-MSBl cells. Restriction endonuclease analysis of polymerase chain reaction (PCR)- amplified DNAs and recombinant plasmids containing DNA inserts specified by CAV that had been passaged 173 times, indicated that the population of high-passage virus was genetically diverse. A 210-base pair (bp) insertion, containing a 19-bp sequence identical to four repeated sequences that are located in the putative non-coding region of the genome was shown to have become established in the virus population by passage number 30. Individual virus isolates that were selected from the high-passage virus population using recombinant DNA cloning and transfection methodologies varied in their pathogenicities. One cloned virus isolate, designated number 10, produced virtually no anaemia and substantially reduced levels of aplasia of the bone marrow and thymus atrophy. The pathogenicity of this isolate was restored following 10 passages in young chicks.     

Molecular characterization of Indian rabies virus isolates by partial sequencing of nucleoprotein (N) and phosphoprotein (P) genes

Rabies is endemic and an important zoonosis in India. There are very few reports available on molecular epidemiology of rabies virus of Indian origin. In this study to know the dynamics of rabies virus, a total of 41 rabies positive brain samples from dogs, cats, domestic animals, wildlife, and humans from 11 states were subjected to RT-PCR amplification of N gene between nucleotide N521-N1262 (742 bp) and P gene between nucleotide P239-P750 (512 bp). The N gene could be amplified from 30, while P gene from 41 samples, using specific sets of primers. The N gene-based phylogenetic analysis indicated that all Indian virus isolates are genetically closely related with a single cluster under arctic/arctic-like viruses. However, two distinct clusters were realized in P gene-based phylogeny viz., Rabies virus isolates of Punjab and Rabies virus isolates of remaining parts of India (other than Punjab). All the Indian rabies virus isolates were closely related to geography (>95% homology), but not to host species.     

Genetic diversity of chicken anemia virus following cell culture passaging in MSB-1 cells

It has been shown that a chicken anemia virus (CAV) isolates which had undergone 60 passages in MSB-1 cells (SMSC-1/P60, 3-1/P60) acquired 33-66 nucleotide substitutions at the coding region resulting in 13-16 amino acid changes as compared to the CAV isolates passaged only 5 times in MSB-1 cells (SMSC-1 and 3-1) (Chowdhury et al., Arch. Virol. 148, 2437-2448, 2003). In this study we found that a low CAV (BL-5) and a high CAV passage (BL-5/P90) differed by only 15 nucleotide substitutions resulting in 11 amino acid changes. Phylogenetic analysis based on VP1 also revealed that both isolates were close to each other but not to other CAV isolates from Malaysia, namely SMSC-1 and 3-1.     

Molecular characterization of the chicken anaemia viruses isolated from broiler farms of west Azerbaijan,Iran

Chicken anaemia virus (CAV) is an economically important pathogen of chickens with worldwide distribution. CAV is the causative agent of chicken anaemia disease, causing severe anaemia, lymphoid atrophy and immunosuppression in young birds. In the present study, the genetic variation of circulating CAVs in west Azerbaijan broiler farms was investigated and compared with CAVs from other countries. Extracted viral DNA from livers of chickens positive for CAV (46 out of 100) was used and a fragment of the VP1 gene 1390 base pairs in size was amplified. The purified products were subjected to restriction fragment-length polymorphism (RFLP) using HinfI endonuclease and nucleotide sequencing. Four different RFLP patterns were identified from all examined CAV DNAs. Sequence analysis of the VP1 gene of isolated CAV viruses revealed a high genetic distance (0.5 to 4.7%) among CAV isolates. Phylogenetic analysis showed that CAVs isolated from Iranian poultry farms clustered with CAVs isolated from different parts of the world. It was concluded that the circulating CAVs in broiler farms of west Azerbaijan had a high genomic variation.     

Effect of multiple cell culture passages on the biological behaviour of chicken anaemia virus.

The Cux-1 isolate of chicken anaemia virus (CAV) was passaged over 320 times in Marek's disease virus transformed chicken lymphoblastoid (MDCC-MSB1) cells. Comparison of the infectivity titres of virus pools derived from viruses that had received 0 (P0), 49 (P49), 170 (P170) and 320 (P320) passages in our laboratory indicated that the yields of infectious virus increased over 100-fold with passage number from P0 to P170. P320 exhibited unusual cell culture growth characteristics in that, unlike its lower passage counterparts, virus-specific immunofluorescence (IF) and cytopathic effect were detected at very low levels at 2 days post infection, with an additional passage of infected cells into fresh medium being required to produce high levels of infectious virus. Experimental infection of 1-day-old SPF chicks showed that P170 and P320 were substantially attenuated compared to P49 and a pathogenic, low-passage isolate used as control. When assessed by the indirect IF test, infection of 1-day-old chicks with the P49 and P170 isolates elicited similar levels of CAV-specific antibody to those elicited by infection with the pathogenic, low-passage virus and higher than those elicited by infection with the P320 isolate. Experimental infection of 5-week-old chicks indicated that the attenuated P170 and P320 isolates invoked similar CAV-specific antibody levels to those invoked by the pathogenic P49 and control isolates.     

Serological and pathogenic characterization of avian reoviruses isolated in Quebec

Reoviruses were isolated from intestinal contents of broiler chickens from nine flocks in Quebec with malabsorption syndrome. Serum neutralization test demonstrated the existence of antigenic differences between the isolates and the reference vaccine strain. The isolated reoviruses were inoculated orally and into the foot pad in one-day-old chicks, resulting in a transient, but significant depression in body weight gains. Chickens infected with isolate 615, showed in addition to growth problems, clinical signs and tissue lesions similar to those observed in field cases. When isolate 615 was inoculated into SPF chicks at one day of age, intestinal absorption of D-xylose in infected chicks at 7 days post-infection was significantly lower (P <0.05) than for corresponding controls. This study suggests the implication of some reovirus isolates, such as 615 which was serologically distinct from the vaccine strain S1133, as infectious agents associated with pathological conditions other than viral arthritis.     

Structure of the Ockelbo virus genome and its relationship to other Sindbis viruses.

Ockelbo virus was first isolated in 1982 in Sweden. It is the causal agent of disease in humans characterized by arthritis, rash, and fever and is antigenically very closely related to Sindbis virus. We have determined the nucleotide and translated amino acid sequences of the prototype Ockelbo virus isolate (82-5) to determine the relatedness of Ockelbo virus to Sindbis virus at the genomic level and clarify the taxonomic position of Ockelbo virus within the alphavirus genus. The numbers of nucleotides and of translated amino acids in each region of the Ockelbo virus genome were exactly the same as those for the prototype AR339 strain of Sindbis virus except for three small deletions and insertions in the C-terminal half of nsP3 and for three single nucleotide insertions and deletions in the 3' untranslated region. Overall there were 672 nucleotide differences (5.7% divergence), resulting in 97 amino acid changes (2.6% divergence), between the two viruses: more than 85% of the nucleotide changes were silent. Only the C-terminal domain of nsP3 and the E2 glycoprotein showed a higher degree of amino acid substitution than the overall average. The former domain is not conserved among alphaviruses, and the latter is primarily responsible for antigenic variation. Sequence analysis of 420 nucleotides at the 3' end of a number of other Sindbis-like alphaviruses, including Karelian fever virus and South African, Indian, and Australian isolates of Sindbis virus, demonstrated that Ockelbo virus is more closely related to South African strains of Sindbis virus than it is to the prototypic Egyptian AR339 strain. Thus the South African strains, which have caused epidemic disease in humans, may have been introduced into Northern Europe by man or by migratory birds to establish Ockelbo disease there. The Indian and Australian strains form a distinct branch of the evolutionary tree and differ from prototypic AR339 Sindbis virus in 17% of the nucleotides sequenced.     

Phylogenetic analysis of the long terminal repeat of feline immunodeficiency viruses from Japan,Argentina and Australia

Summary The nucleotide sequences of the long terminal repeat of five Japanese, five Argentine and three Australian isolates of feline immunodeficiency virus (FIV) were determined and compared with those of isolates previously described. The results revealed that the Japanese isolates were found to cluster with nucleotide sequence similarity of 95.6%–99.4%. The Australian isolates also clustered with nucleotide sequence similarity of 97.2%–99.4%. The Argentine isolates formed two groups; the LP9 isolate is closely related to the Japanese isolates, whereas the LP1, LP3, LP20 and LP24 isolates are distant from both the Japanese and Australian isolates. From these results, FIV can be divided into three groups, namely: (I) the Californian, Australian and British isolates; (II) the Japanese isolates and one Argentine LP9 isolate; (III) the other Argentine isolates.     

Astrovirus-induced “white chicks” condition – field observation,virus detection and preliminary characterization

Chicken astrovirus (CAstV) was recently indicated as the factor of the “white chicks” condition associated not only with increased embryo/chick mortality but also with weakness and white plumage of hatched chicks. In February 2014, organ samples (livers and kidneys) from dead-in-shell embryos, as well as 1-day-old whitish and normal chicks, were delivered from one hatchery in Poland for disease diagnosis. The samples originated from the same 30-week-old breeder flock in which the only observed abnormal signs were 4–5% decrease in the number of hatched chickens and the presence (about 1%) of weaker chicks with characteristic whitish plumage among normal ones. CAstV was detected in submitted samples and was then isolated in 10-day-old embryonated specific pathogen free (SPF) chicken eggs. We also reproduced an infection model for the “white chicks” condition in SPF layer chickens using the isolated PL/G059/2014 strain as the infectious agent. Results of experimental reproduction of the “white chicks” condition were somewhat more serious than field observation. The administration of the CAstV material into the yolk sac of 8-day-old SPF chicken eggs caused delay and prolongation of hatching, as well as death of embryos/chicks, and also a change of plumage pigmentation. Only two chicks of a total of 10 inoculated SPF eggs survived and were observed for 2 months. A gradual elimination of the CAstV genome was noted in this period. Moreover, a few contact-naive SPF chicks, which had been placed in the same cage, were infected with CAstV. Molecular characterization of detected CAstV was performed by nucleotide sequencing of the full ORF2 region encoding the capsid precursor protein gene. Phylogenetic studies showed that the PL/G059/2014 isolate clustered in the subgroup Aiii of CAstV. In the light of the new classification rules, the Polish PL/G059/2014 CAstV isolate could be assigned to a new species of the Avastrovirus genus.     

Molecular characterization of a wild poliovirus type 3 epidemic in The Netherlands (1992 and 1993).

An outbreak of poliomyelitis due to wild poliovirus type 3 (PV3) occurred in an unvaccinated community in The Netherlands between September 1992 and February 1993. The outbreak involved 71 patients. The aim of this study was to characterize the virus at the molecular level and to analyze the molecular evolution of the epidemic virus. Molecular analysis was carried out by sequencing the VP1/2A junction region (150 nucleotides) of 50 PV3 strains isolated in association with this outbreak and the entire VP1 gene of 14 strains. In addition, the sequence of the VP1/2A junction region of strains from geographical regions endemic for PV3 (Egypt, India, and Central Asia) was analyzed and compared with the nucleotide sequence of the epidemic strain from The Netherlands. The earliest isolate was obtained from river water sampled 3 weeks before diagnosis of the first poliomyelitis patient and was found by VP1/2A sequence analysis to be genetically identical to the strain isolated from the first patient. Sequence divergence among the strains from the epidemic in The Netherlands was less than 2%. The closest genetic similarity (97.3%) was found with an Indian isolate (New Delhi, December 1991), indicating the likely source of the virus. A more than 99% sequence similarity was found in the VP1/2A region. Finally, the sequence information was used to design primers for the specific and highly sensitive molecular detection of PV3 strains during the epidemic.     

Evidence of bluetongue virus serotype 21 (BTV-21) divergence

Bluetongue virus serotype 21 (BTV-21) was originally isolated from Australia, but has now been reported from India, Indonesia, China and Japan. We report the isolation, and sequencing of BTV-21 from India. The complete ORF sequence of VP2 gene of this isolate showed that it is closely related to recent BTV-21 isolates from Japan (93–94% identity), and distantly related to BTV-21 reference strain (86% identity). Our results, along with the available sequences of Japanese isolates, suggest that the currently circulating BTV-21 strains from India and Japan are divergent from the original strain(s) from Australia and shed light on designing molecular diagnostics for the detection of BTV.